These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Jerkass Woobie: Sterling Von Oxnard in "My Fair Rebound". He tries to sabotage Rebound during the dog show, but only because he thinks that, if he loses, his owner will put him up for sale. Why? Because that's what most of his previous owners did. It makes it much more satisfying when Mildred finally starts showing him some love at the end of the episode.
The episode "No Dogs Allowed" even was a Shout Out to the bronies, with the message being that there can be room in your heart for both ponies and puppies.
Relationship Writing Fumble / No Yay: In "Mutternal Instincts", Cookie and Cupcake are like mother and daughter (or sisters). Their relationship is actually pretty well written, except for how the dogs refer to Cookie's and Cupcake's bonding as falling in love.
Romance is the usual way many think of "falling in love", but it isn't always; it just depends on how you think of the phrase.
Tear Jerker: In Toyoshiko!, Toyoshiko basically commits suicide by jumping into a large magnet, thus erasing her memory. Sure, at the end of the episode, Strudel 'repairs' her, but all she did was make another Toyoshiko, it's not the same Toyoshiko. Her memories are gone, and our personalities are, to a significant degree, decided by our memories. Eventually, the original Toyoshiko's personality and the new Toyoshiko's personalities will have diverged, although Strudel won't notice, because the original Toyoshiko didn't live long enough for her memories to develop her base personality. Also, she never appears in another episode, which is odd, considering she's supposedly the only one to really understand Strudel.
Tough Act to Follow: The creators also made Recess, considered to be one of the best (if not the best) cartoons of the late 90's, and fans expecting something exactly like it were a bit disappointed.
Uncanny Valley: Some characters (especially the humans and a few animals) look weird due to a strange mix of "cutesy" and "cartoonish".
Viewer Gender Confusion: Patches. He/she sounds like a girl (obviously because he/she is voiced by one), yet he/she is often referred to as male. Which is it?
The Woobie: Yipper from the episode The Yipper Caper. He spends most of the episode with low self esteem, whimpering because he thinks nobody wants him. Of course, he gets a happy ending but just watching in the the beginning and middle parts of the episode is enough to want to cuddle him.